:( There is an unfortunate bug anyhow with ammo and reloading: If your smallest stack is smaller than the weapon magazine(s) you're trying to reload, your weapon(s) will not be fully reloaded. This goes for everything: plasma rifles, chainguns, pistols, etc. Fortunately, this is going to be fixed in the next release so that if you've got another stack, that will get dipped into as well as the nearly empty one so you won't have any more partial reloads.